Statistical Methods in Topological Data Analysis for Complex, High-Dimensional Data

The utilization of statistical methods an their applications within the new field of study known as Topological Data Analysis has has tremendous potential for broadening our exploration and understanding of complex, high-dimensional data spaces. This paper provides an introductory overview of the mathematical underpinnings of Topological Data Analysis, the workflow to convert samples of data to topological summary statistics, and some of the statistical methods developed for performing inference on these topological summary statistics. The intention of this non-technical overview is to motivate statisticians who are interested in learning more about the subject.Comment: 15 pages, 7 Figures, 27th Annual Conference on Applied Statistics in Agricultur

GPU Accelerated Discontinuous Galerkin Methods for Shallow Water Equations

We discuss the development, verification, and performance of a GPU accelerated discontinuous Galerkin method for the solutions of two dimensional nonlinear shallow water equations. The shallow water equations are hyperbolic partial differential equations and are widely used in the simulation of tsunami wave propagations. Our algorithms are tailored to take advantage of the single instruction multiple data (SIMD) architecture of graphic processing units. The time integration is accelerated by local time stepping based on a multi-rate Adams-Bashforth scheme. A total variational bounded limiter is adopted for nonlinear stability of the numerical scheme. This limiter is coupled with a mass and momentum conserving positivity preserving limiter for the special treatment of a dry or partially wet element in the triangulation. Accuracy, robustness and performance are demonstrated with the aid of test cases. We compare the performance of the kernels expressed in a portable threading language OCCA, when cross compiled with OpenCL, CUDA, and OpenMP at runtime.Comment: 26 pages, 51 figure

Detection of equine atypical myopathy-associated hypoglycin A in plant material: Optimisation and validation of a novel LC-MS based method without derivatisation

Hypoglycin A (HGA) toxicity, following ingestion of material from certain plants, is linked to an acquired multiple acyl-CoA dehydrogenase deficiency known as atypical myopathy, a commonly fatal form of equine rhabdomyolysis seen worldwide. Whilst some plants are known to contain this toxin, little is known about its function or the mechanisms that lead to varied HGA concentrations between plants. Consequently, reliable tools to detect this amino acid in plant samples are needed. Analytical methods for HGA detection have previously been validated for the food industry, however, these techniques rely on chemical derivatisation to obtain accurate results at low HGA concentrations. In this work, we describe and validate a novel method, without need for chemical derivatisation (accuracy = 84–94%; precision = 3–16%; reproducibility = 3–6%; mean linear range R2 = 0.999). The current limit of quantitation for HGA in plant material was halved (from 1μg/g in previous studies) to 0.5μg/g. The method was tested in Acer pseudoplatanus material and other tree and plant species. We confirm that A. pseudoplatanus is most likely the only source of HGA in trees found within European pastures

Two-sided asymmetric subduction; implications for tectonomagmatic and metallogenic evolution of the Lut Block, Eastern Iran

West directed subduction zones show common characteristics, such as low structural elevation, deep trench, steep slab and a conjugate back-arc basin that are opposite to those of the east directed subduction zones. The tectonomagmatic and metallogenic setting of the Lut Block is still a matter of debate and several hypotheses have been put forward. Despite some authors denying the influence of the operation of Benioff planes, the majority propose that it occurred beneath the Afghan Block, while others consider that oceanic lithosphere was dragged under the Lut Block. Cu-Au porphyry deposits seem to occur in an island arc geotectonic setting during the middle Eocene while Mo-bearing deposits are coincident with the crustal thickening during Oligocene. We introduce new trace element and isotope geochemical data for granitoids and structural evidences testifying the two-sided asymmetric subduction beneath both Afghan and Lut Blocks, with different rates of consumption of oceanic lithosphere

Novel application assigned to toluquinol: inhibition of lymphangiogenesis by interfering with VEGF-C/VEGFR-3 signalling pathway

BACKGROUND AND PURPOSE Lymphangiogenesis is an important biological process associated with the pathogenesis of several diseases, including metastatic dissemination, graft rejection, lymphoedema and other inflammatory disorders. The development of new drugs that block lymphangiogenesis has become a promising therapeutic strategy. In this study, we investigated the ability of toluquinol, a 2-methyl-hydroquinone isolated from the culture broth of the marine fungus Penicillium sp. HL-85-ALS5-R004, to inhibit lymphangiogenesis in vitro, ex vivo and in vivo. EXPERIMENTAL APPROACH We used human lymphatic endothelial cells (LECs) to analyse the effect of toluquinol in 2D and 3D in vitro cultures and in the ex vivo mouse lymphatic ring assay. For in vivo approaches, the transgenic Fli1:eGFPy1 zebrafish, mouse ear sponges and cornea models were used. Western blotting and apoptosis analyses were carried out to search for drug targets. KEY RESULTS Toluquinol inhibited LEC proliferation,migration, tubulogenesis and sprouting of new lymphatic vessels. Furthermore, toluquinol induced apoptosis of LECs after 14 h of treatment in vitro, blocked the development of the thoracic duct in zebrafish and reduced the VEGF-C-induced lymphatic vessel formation and corneal neovascularization in mice. Mechanistically, we demonstrated that this drug attenuates VEGF-C-induced VEGFR-3 phosphorylation in a dose-dependentmanner and suppresses the phosphorylation of Akt and ERK1/2. CONCLUSIONS AND IMPLICATIONS Based on these findings, we propose toluquinol as a new candidate with pharmacological potential for the treatment of lymphangiogenesis-related pathologies. Notably, its ability to suppress corneal neovascularization paves the way for applications in vascular ocular pathologies.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. This work has been supported by personal funding by FP7-PEOPLE-2013-IEF Marie Curie Postdoctoral Fellowship (MGC). Acknowledged are the supporting grants from the Action de Recherche Concertée (ARC) (Université de Liège), the Fonds de la Recherche Scientifique-FNRS (F.R.S.-FNRS), the Foundation Against Cancer (foundation of public interest), the Centre Anticancéreux près l’Université de Liège, the Fonds Léon Fredericq (University of Liège), the Interuniversity Attraction Poles Programme-Belgian Science Policy (all from Belgium) and the Plan National Cancer (« Service Public Federal » from Belgium). Research in the lab of A.R.Q. and M.A.M. was supported by grants BIO2014-56092-R (MINECO and FEDER) and P12-CTS-1507 (Andalusian Government and FEDER)

Statistical Methods in Topological Data Analysis for Complex, High-Dimensional Data

The utilization of statistical methods an their applications within the new field of study known as Topological Data Analysis has has tremendous potential for broadening our exploration and understanding of complex, high-dimensional data spaces. This paper provides an introductory overview of the mathematical underpinnings of Topological Data Analysis, the workflow to convert samples of data to topological summary statistics, and some of the statistical methods developed for performing inference on these topological summary statistics. The intention of this non-technical overview is to motivate statisticians who are interested in learning more about the subject